DOI: 10.1093/bioinformatics/btk005. EDGE: extraction and analysis of differential gene expression

EDGE: extraction and analysis of differential gene expression

10.1093/bioinformatics/btk005

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: EDGE (Extraction of Differential Gene Expression) is an open source, point-and-click software program for the significance analysis of DNA microarray experiments. EDGE can perform both standard and time course differential expression analysis. The functions are based on newly developed statistical theory and methods. This document introduces the EDGE software package. Availability: EDGE is freely available for non-commercial users. EDGE can be downloaded for Windows, Macintosh and Linux/UNIX from Contact: jtleek@u.washington.edu

Bibliography

Leek, J. T., Monsen, E., Dabney, A. R., & Storey, J. D. (2005). EDGE: extraction and analysis of differential gene expression. Bioinformatics, 22(4), 507â508.

Authors 4

Jeffrey T. Leek (first)
Eva Monsen (additional)
Alan R. Dabney (additional)
John D. Storey (additional)

References 13 Referenced 208

10.1073/pnas.97.18.10101 / Proc. Natl Acad. Sci. / Singular value decomposition for genome-wide expression data processing and modeling by Alter (2000)
10.1093/biostatistics/kxh018 / Biostatistics / Improved statistical tests for differential gene expression by shrinking variance components estimates by Cui (2005)
10.1198/016214502753479248 / J. Am. Stat. Assoc. / Comparison of discrimination methods for the classification of tumors using gene expression data by Dudoit (2002)
10.1198/016214501753382129 / J. Am. Stat. Assoc. / Empirical Bayes analysis of a microarray experiment by Efron (2001)
10.1073/pnas.95.25.14863 / Proc. Natl Acad. Sci. / Cluster analysis and display of genome-wide expression patterns by Eisen (1998)
10.1056/NEJM200102223440801 / N. Engl. J. Med. / Gene-expression profiles in hereditary breast cancer by Hedenfalk (2002)
{'key': '2023012408514516600_b7', 'first-page': '31', 'article-title': 'Replicated microarray data', 'volume': '12', 'author': 'Lonnstedt', 'year': '2002', 'journal-title': 'Stat. Sinica'} / Stat. Sinica / Replicated microarray data by Lonnstedt (2002)
{'key': '2023012408514516600_b8', 'volume-title': 'R: A language and environment for statistical computing', 'author': 'R Development Core Team', 'year': '2005'} / R: A language and environment for statistical computing by R Development Core Team (2005)
{'key': '2023012408514516600_b9', 'article-title': 'The optimal discovery procedure: a new approach to simultaneous significance testing', 'volume': '259', 'author': 'Storey', 'year': '2005', 'journal-title': 'UW Biostatistics Working Paper Series Working Paper'} / UW Biostatistics Working Paper Series Working Paper / The optimal discovery procedure: a new approach to simultaneous significance testing by Storey (2005)
10.1073/pnas.1530509100 / Proc. Natl Acad. Sci. / Statistical significance for genome-wide studies by Storey (2003)
{'key': '2023012408514516600_b11', 'article-title': 'The Optimal Discovery Procedure for Large-Scale Significance Testing, with Applications to Comparative Microarray Experiments', 'volume-title': 'UW Biostatistics Working Paper Series', 'author': 'Storey', 'year': '2005'} / UW Biostatistics Working Paper Series / The Optimal Discovery Procedure for Large-Scale Significance Testing, with Applications to Comparative Microarray Experiments by Storey (2005)
10.1073/pnas.0504609102 / Proc. Natl Acad. Sci. / Significance analysis of time course microarray experiments by Storey (2005)
10.1093/bioinformatics/17.6.520 / Bioinformatics / Missing value estimation methods for DNA microarrays by Troyanskaya (2001)

Dates

Type	When
Created	19 years, 8 months ago (Dec. 15, 2005, 8:24 p.m.)
Deposited	2 years, 7 months ago (Jan. 24, 2023, 4:25 a.m.)
Indexed	1 week, 6 days ago (Aug. 12, 2025, 5:51 p.m.)
Issued	19 years, 8 months ago (Dec. 15, 2005)
Published	19 years, 8 months ago (Dec. 15, 2005)
Published Online	19 years, 8 months ago (Dec. 15, 2005)
Published Print	19 years, 6 months ago (Feb. 15, 2006)

Funders 0

None

BibTeX

@article{Leek_2005, title={EDGE: extraction and analysis of differential gene expression}, volume={22}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btk005}, DOI={10.1093/bioinformatics/btk005}, number={4}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Leek, Jeffrey T. and Monsen, Eva and Dabney, Alan R. and Storey, John D.}, year={2005}, month=dec, pages={507–508} }

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